// -*- mode: c++; indent-tabs-mode: nil; -*-
//
// Copyright (c) 2017 Illumina, Inc.
// All rights reserved.

// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:

// 1. Redistributions of source code must retain the above copyright notice, this
//    list of conditions and the following disclaimer.

// 2. Redistributions in binary form must reproduce the above copyright notice,
//    this list of conditions and the following disclaimer in the documentation
//    and/or other materials provided with the distribution.

// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
// ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
// WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
// DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
// OR TORT INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

/**
 * \brief Implementation detail structure for Klib-type alignments
 *
 * \file KlibImpl.hh
 * \author Peter Krusche
 * \email pkrusche@illumina.com
 *
 */

#pragma once

extern "C" {
#include "ksw.h"
}

#include <boost/core/noncopyable.hpp>
#include <cstdlib>
#include <cstring>
#include <memory>
#include <sstream>

namespace common
{

// [INCLUDED CODE START]
// The following code was copied from
//
//  https://github.com/ekg/gssw/blob/master/src/ssw_cpp.cpp
//
// Distributed under MIT license:
// Copyright (c) 2012-2015 Boston College
// Permission is hereby granted, free of charge,
// to any person obtaining a copy of this software and associated
// documentation files (the "Software"), to deal in the Software without
// restriction, including without limitation the rights to use, copy, modify,
// merge, publish, distribute, sublicense, and/or sell copies of the Software,
// and to permit persons to whom the Software is furnished to do so, subject
// to the following conditions:
// The above copyright notice and this permission notice shall be included
// in all copies or substantial portions of the
// Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
// IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
// CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
// TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
// SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

static int8_t translation_matrix[128]
    = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
        4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
        //   A     C            G
        4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
        //             T
        4, 4, 4, 4, 3, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
        //   a     c            g
        4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
        //             t
        4, 4, 4, 4, 3, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 };

static inline int translate(const char* bases, uint8_t* translated, int length)
{
    char* ptr = (char*)bases;
    int len = 0;

    for (int i = 0; i < length; ++i)
    {
        translated[i] = translation_matrix[((int)*ptr) & 0x7f];
        ++ptr;
        ++len;
    }

    return len;
}
// [INCLUDED CODE END]

struct KlibAlignmentImpl : boost::noncopyable
{
    KlibAlignmentImpl()
        : gapo(0)
        , gape(0)
        , reflen(0)
        , altlen(0)
        , valid_result(false)
        , cigar_len(0)
        , cigar(NULL)
        , qprofile(NULL)
    {
        memset(mat, 0, 25);
    }

    ~KlibAlignmentImpl()
    {
        if (qprofile)
        {
            free(qprofile);
        }
        if (cigar)
        {
            free(cigar);
        }
    }

    KlibAlignmentImpl const& operator=(KlibAlignmentImpl const&) = delete;

    int8_t mat[25];
    int gapo;
    int gape;

    std::shared_ptr<uint8_t> ref;
    int reflen;

    std::shared_ptr<uint8_t> alt;
    int altlen;

    bool valid_result;

    kswr_t result;
    int cigar_len;
    uint32_t* cigar;

    kswq_t* qprofile;
};
}
